[Bioc-devel] InteractionSet for structural variants

[Aaron Lun]

> Thanks for your response. So far my intention is to to plot them and I
> do not intend on performing any other operation. The first step would be
> read in the VCF file and transform it into a meaningful object and I was
> hoping there was a core package already taking care of that, but I get
> from your answer that there's no such functionality implemented.

Not to my knowledge... but if you're planning on writing some relevant 
functions, I'm sure we could find a home for it somewhere.

-A

> El 5/18/19 a las 4:47 AM, Aaron Lun escribió:
>> I would say that it depends on what operations you intend to perform
>> on them. You can _store_ things any way you like, but the trick is to
>> ensure that operations and manipulations on those things are
>> consistent and meaningful. It is not obvious that there are meaningful
>> common operations that one might want to apply to all structural
>> variants.
>>
>> For example, translocations involve two genomic regions (i.e., the two
>> bits that get stuck together) and so are inherently two-dimensional. A
>> lot of useful operations will be truly translocation-specific, e.g.,
>> calculation of distances between anchor regions, identification of
>> bounding boxes in two-dimensional space. These operations will be
>> meaningless to 1-dimensional variants on the linear genome, e.g.,
>> CNVs, inversions. The converse also applies where operations on the
>> linear genome have no single equivalent in the two-dimensional case.
>>
>> So, I would be inclined to store them separately. If you must keep
>> them in one object, just lump them into a List with "translocation"
>> (GInteractions), "cnv" (GRanges) and "inversion" (another GRanges)
>> elements, and people/programs can pull out bits and pieces as needed.
>>
>> -A
>>
>>
>> On 5/17/19 4:38 AM, Bernat Gel Moreno wrote:
>>> Hi all,
>>>
>>> Is there any standard recommended container for genomic structural
>>> variants? I think InteractionSet would work fine for translocation and
>>> GRanges for inversions and copy number changes, but I don't know what
>>> would be the recommended way to store them all together using standard
>>> Bioconductor objects.
>>>
>>> And actually, is there any package that would load a SV VCF by lumpy or
>>> delly and build that object?
>>>
>>> Thanks!
>>>
>>> Bernat
>>>
>>>
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>>
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